NGS has been available for more than 10 years, and, through NGS, we have discovered a long list of both common and uncommon genetic mutations that occur in patients with CLL. Common mutations are found in approximately 10% to 15% of patients with CLL in the frontline setting and include NOTCH1, XPO1, TP53, and ATM mutations. Uncommon mutations are found in less than 5% of patients with CLL and include POT1, EGR2, and PTPN11 mutations. 

Most of these uncommon mutations occur so infrequently that it will be difficult to determine their influence on a patient's response without relying on merged results from multiple clinical trials to build a large enough sample. For instance, do the uncommon NFKBIE or PTPN11 mutations correlate with disease progression in individuals on Bruton tyrosine kinase inhibitor therapy? And do the uncommon PTPN11 or RAS mutations, both of which activate the MAPK pathway, correlate with resistance to venetoclax in patients with CLL like they do in those with myeloid malignancies? 

We have learned about responses to treatment associated with the more common mutations, but some of the markers from the chemoimmunotherapy era had to be reevaluated in the context of novel agents and targeted therapies. The NOTCH1 mutation has been linked to high-risk CLL and Richter transformation, and we are still learning about the significance of these mutations in different contexts, with differing sets of coexisting genetic anomalies, and in the era of targeted therapies. The common SF3B1 and XPO1 mutations are not necessarily associated with progression on targeted drugs, but why is that? The NOTCH1 mutation is clearly associated with a specific biologic activity. It downregulates CD20 expression, and there does not appear to be benefits in adding an anti-CD20 antibody to chemoimmunotherapy in patients with this mutation. Now, will this association apply to patients receiving venetoclax and obinutuzumab, venetoclax and rituximab, or acalabrutinib and obinutuzumab? We do not yet know. To date, there have been few studies incorporating anti-CD20 antibodies that are equipped to answer these questions. 

There has been great progress, but there is still a lot to learn, even with some of the more common mutations in CLL. Drawing on combined data over the next several years, we hope to better understand the significance of uncommon mutations and their treatment implications.

Germline mutations are fairly uncommon in patients with CLL, but they are something that we should be watchful for. The frequency of germline variants in ATM appears to be relatively unique to patients with CLL compared with individuals with other hematologic malignancies. If you do the sequencing and find a very high variant allele frequency of a genetic abnormality of interest (eg, 40%-60%), this is consistent with a mutation at a heterozygous frequency, and this might correspond to a germline mutation. Such a germline mutation, if present, may have predisposed the patient to CLL and warrants a referral for genetic counseling because it may increase the risk for other cancer types.